I am trying to connect to a mainframe from linux server using
sftp -b $batch_file user@remote_user
There is no equivalent of FTP's
SITE command in SFTP. SFTP uses a binary format for its protocol messages, and uses specific request numbers (or IDs) to indicate the desired operation. And SFTP does not define any request number/ID for "execute this string as a command". SSH can be used for that sort of thing, but not SFTP.